while there are some AA knowledgeable folks in here, the AA forum is probably the right spot for these questions for the two of you. Practically, from Asia Miles / Cathay point of view, of course this (the act of getting an upgrade) is possible...just enter your Asia Miles # at booking and use AM to upgrade the ticket. Provided you're in the proper fare class (W/R) and redemption availability is there, it will process. However, I suspect your question is more "will I still get AA points for my underlying fare class when I do this", and whether or not the AA system will give you the points for the underlying fare class, or the systems will conspire to screw you over.

You'll definitely be able to strip the CX MPC/Asia Miles number from the booking once you're confirmed and ticketed, and presumably can add your AA number. However, whether or not AA mucks it up afterwards is another story and probably a question for that forum. Even if you strip the FF #, I've seen reports in here where the original program that was stripped is still credited, even though you changed the FF #. I am not sure what AA's systems are like in this situation.